[2023-03-16 09:23:09,461] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:23:09,461] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:23:09,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ef6425d-74ff-43bf-b2bf-eae6733644f8/dqc_reference
[2023-03-16 09:23:11,217] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:23:11,218] [INFO] Task started: Prodigal
[2023-03-16 09:23:11,218] [INFO] Running command: cat /var/lib/cwl/stg1f0f6b89-ef83-4955-91f4-f9270fcf7c82/OceanDNA-b20908.fa | prodigal -d OceanDNA-b20908/cds.fna -a OceanDNA-b20908/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:24:09,108] [INFO] Task succeeded: Prodigal
[2023-03-16 09:24:09,108] [INFO] Task started: HMMsearch
[2023-03-16 09:24:09,109] [INFO] Running command: hmmsearch --tblout OceanDNA-b20908/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ef6425d-74ff-43bf-b2bf-eae6733644f8/dqc_reference/reference_markers.hmm OceanDNA-b20908/protein.faa > /dev/null
[2023-03-16 09:24:09,463] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:24:09,463] [INFO] Found 6/6 markers.
[2023-03-16 09:24:09,527] [INFO] Query marker FASTA was written to OceanDNA-b20908/markers.fasta
[2023-03-16 09:24:09,529] [INFO] Task started: Blastn
[2023-03-16 09:24:09,529] [INFO] Running command: blastn -query OceanDNA-b20908/markers.fasta -db /var/lib/cwl/stg1ef6425d-74ff-43bf-b2bf-eae6733644f8/dqc_reference/reference_markers.fasta -out OceanDNA-b20908/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:24:10,142] [INFO] Task succeeded: Blastn
[2023-03-16 09:24:10,148] [INFO] Selected 24 target genomes.
[2023-03-16 09:24:10,148] [INFO] Target genome list was writen to OceanDNA-b20908/target_genomes.txt
[2023-03-16 09:24:10,185] [INFO] Task started: fastANI
[2023-03-16 09:24:10,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f0f6b89-ef83-4955-91f4-f9270fcf7c82/OceanDNA-b20908.fa --refList OceanDNA-b20908/target_genomes.txt --output OceanDNA-b20908/fastani_result.tsv --threads 1
[2023-03-16 09:24:31,237] [INFO] Task succeeded: fastANI
[2023-03-16 09:24:31,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ef6425d-74ff-43bf-b2bf-eae6733644f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:24:31,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ef6425d-74ff-43bf-b2bf-eae6733644f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:24:31,248] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:24:31,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:24:31,249] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.2132	576	3104	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.8567	541	3104	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.8413	558	3104	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	75.2031	62	3104	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.126	323	3104	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	75.0549	97	3104	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	74.9661	76	3104	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	74.9592	116	3104	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.9128	176	3104	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	74.9077	83	3104	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	74.8565	145	3104	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.8514	328	3104	95	below_threshold
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	74.7665	74	3104	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.7293	167	3104	95	below_threshold
Paenibacillus pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	74.7289	84	3104	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	74.7191	89	3104	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	74.7079	54	3104	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	74.6954	82	3104	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	74.5255	51	3104	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	74.5225	50	3104	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:24:31,411] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20908/tc_result.tsv
[2023-03-16 09:24:31,419] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:24:31,419] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:24:31,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ef6425d-74ff-43bf-b2bf-eae6733644f8/dqc_reference/checkm_data
[2023-03-16 09:24:31,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:24:31,501] [INFO] Task started: CheckM
[2023-03-16 09:24:31,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20908/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20908/checkm_input OceanDNA-b20908/checkm_result
[2023-03-16 09:26:48,759] [INFO] Task succeeded: CheckM
[2023-03-16 09:26:48,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:26:48,785] [INFO] ===== Completeness check finished =====
[2023-03-16 09:26:48,785] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:26:48,785] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20908/markers.fasta)
[2023-03-16 09:26:48,786] [INFO] Task started: Blastn
[2023-03-16 09:26:48,786] [INFO] Running command: blastn -query OceanDNA-b20908/markers.fasta -db /var/lib/cwl/stg1ef6425d-74ff-43bf-b2bf-eae6733644f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20908/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:26:49,756] [INFO] Task succeeded: Blastn
[2023-03-16 09:26:49,763] [INFO] Selected 16 target genomes.
[2023-03-16 09:26:49,763] [INFO] Target genome list was writen to OceanDNA-b20908/target_genomes_gtdb.txt
[2023-03-16 09:26:49,782] [INFO] Task started: fastANI
[2023-03-16 09:26:49,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f0f6b89-ef83-4955-91f4-f9270fcf7c82/OceanDNA-b20908.fa --refList OceanDNA-b20908/target_genomes_gtdb.txt --output OceanDNA-b20908/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:27:09,850] [INFO] Task succeeded: fastANI
[2023-03-16 09:27:09,859] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:27:09,860] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_001464385.1	s__Ga0077550 sp001464385	76.6368	687	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	76.5664	655	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_013812955.1	s__Nannocystis sp013812955	76.2394	330	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	76.211	578	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	76.0519	470	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_003696955.1	s__J032 sp003696955	75.9891	218	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__J032	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994615.1	s__Enhygromyxa salina_A	75.9367	504	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793465.1	s__Nannocystis sp016793465	75.8949	580	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002343915.1	s__Nannocystis exedens	75.8322	557	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000737335.2	s__Enhygromyxa salina_C	75.7718	436	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	75.7686	508	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	75.5141	309	3104	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903914615.1	s__Rubrivivax sp903914615	74.8958	128	3104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005774595.1	s__D1FN1-002 sp005774595	74.7262	53	3104	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__OPB41;f__D1FN1-002;g__D1FN1-002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004793665.1	s__NM07-P-09 sp004793665	74.7045	53	3104	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__NM07-P-09	95.0	99.12	98.60	0.95	0.93	6	-
GCA_902826345.1	s__CADEEN01 sp902826345	74.5809	93	3104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CADEEN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:27:09,868] [INFO] GTDB search result was written to OceanDNA-b20908/result_gtdb.tsv
[2023-03-16 09:27:09,883] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:27:09,890] [INFO] DFAST_QC result json was written to OceanDNA-b20908/dqc_result.json
[2023-03-16 09:27:09,890] [INFO] DFAST_QC completed!
[2023-03-16 09:27:09,890] [INFO] Total running time: 0h4m0s